This article adapts the Evidence-Based Reasoning (EBR) Framework (Brown, Furtak, Timms, Nagashima, & Wilson, this issue) to create a coding system for assessing argumentation in science classroom discourse. The instrument, "Evidence-Based Reasoning in Science Classroom Discourse", is intended to provide a means for measuring the quality of EBR in whole-class discussions, capturing teachers' and students' co-constructed reasoning about scientific phenomena. This article describes the features of the instrument, illustrates how it can be applied to an instance of classroom discussion, explores its strengths and weaknesses, and makes recommendations for future analyses. It combines previous frameworks that focused on structure of arguments and epistemic quality with a framework for analyzing the teacher's contribution to reasoning to form a new analytic tool for assessing students' ability to construct evidence-supported arguments in science classroom discourse. (Contains 8 tables and 1 figure.)